Research workbench
Crystal structure of human papillomavirus type 59 L1 pentamer
Analyse Crystal structure of human papillomavirus type 59 L1 pentamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J6R
- Type
- protein
- Length
- 4,190 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein L1
- UniProt
- Q81971
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, G, I, J | Major capsid protein L1 | protein | 420 | 13% helix, 35% strand | Q81971 |
| B | Major capsid protein L1 | protein | 416 | 13% helix, 36% strand | Q81971 |
| H | Major capsid protein L1 | protein | 414 | 14% helix, 36% strand | Q81971 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.77 | 0.79 | 95 | empty |
| 2 | 955 | 0.77 | 0.79 | 95 | empty |
| 3 | 50 | 0.71 | 0.99 | 31 | empty |
| 4 | 335 | 0.64 | 0.80 | 37 | empty |
| 5 | 302 | 0.63 | 0.80 | 40 | empty |
Interfaces
25 interfaces between chains.
- G–I · 3733 Ų buried · 57 hydrogen bonds · protein-protein
- E–I · 3733 Ų buried · 57 hydrogen bonds · protein-protein
- A–B · 3732 Ų buried · 58 hydrogen bonds · protein-protein
- F–J · 3730 Ų buried · 58 hydrogen bonds · protein-protein
- D–H · 3722 Ų buried · 57 hydrogen bonds · protein-protein
Compared structures
- 5J6R · Crystal structure of Human Papillomavirus Type 59 L1 pentamer · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q81971
- Elsewhere: RCSB PDB 5J6R · PDBe 5J6R · UniProt Q81971
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